The Proteomic Analysis DataBase initiative was originally formed as a gateway for the analysis of large-scale biochemical and mass spectrometry screens of biological materials by bioinformatics and Systems Biology.

The first database to be implemented in this framework is UPdb the urinary database listing molecular species (peak maps) observed by mass spectrometry. This database will also serve as a general depository of raw mass spectrometry data from human urine samples, and researchers are encouraged to submit their data by contacting us in the first instance.

Other databases which are live:

LSSR (Large Scale Screening Resource), which is intended to gather existing information of expressed proteins in specific tissues from published articles. This database also contains a peptide mapping database (PepMap), which lists all peptides reportedly found by mass spectrometry screens from molecules listed in LSSR.

CluSO (Clustered sequences and Orthologs), where all protein sequences found in one species (as listed in various sequence databases) are assembled and clustered to generate a fully non-redundant and as-complete-as-possible list of proteins expressed in specific species. This database also contains the HopMap (homologue, orthologue and paralogue maps) database, which serves as an accession number unifier of molecular entries across various species.

Statistics

Updb total entry count: 3895

LSSR total entry count: 77544 (redundant) and 13359 (non-redundant)

PepMap total entry count: more than 500.000

PPID entry count: more than 8000 protein interactions (not deployed at the moment)

CluSO: working on the human protein set, simple datasets such as bacteria and yeast finished (not deployed at the moment)